Proteomics Application Notes

Proteomics Application Notes

IntroductionEfficient, reproducible and rapid tissue disruption and extraction of biomolecules are prerequisite for many biological applications. Solid tissues, especially tough or fibrous ones like muscle, generally require extensive mechanical disruption prior to extraction. Mortar and pestle grinding, pulverization in liquid nitrogen or homogenization with a dounce or polytron homogenizer are some of the classical methods that have been used for tissue disruption. However, these manual methods are often inconsistent, time consuming and potentially hazardous. In addition, due to the amount of sample loss inherent in these methods, they are often unsuitable for use with small samples in the 10 μg size range. Here we describe a system for efficient tissue disruption and extraction of protein or RNA from solid tissues using the Pressure Cycling Technology Sample Preparation System (PCT SPS) and the FT 500-ND PULSE Tubes. Pressurization of small sample volumes in these tubes causes repeated compression of the sample tissue between the PULSE Tube Cap and Ram. This high-pressure mechanical tissue disruption, combined with the power of pressure cycling technology (PCT), is an efficient and reproducible method to prepare whole tissue lysates from solid tissue samples for extraction of proteins or nucleic acids.

Rhodopseudomonas palustris is a Gram negative, purple, non-sulfur, phototropic bacterium, and is a metabolically versatile microbe. The bacterium can grow in the presence or absence of oxygen. In response to environmental changes, it can engage in alternative metabolic processes for cellular respiration. R. palustris can degrade the aromatic compounds comprising lignin, the second most abundant natural polymer. As such, it is being investigated for its potential in the removal of environmental pollutants [1]. The genome of R. palustris has been sequenced and annotated [2]. It follows that the analysis of this microorganism’s proteome has become an active area of research. Reliable proteomic analysis is contingent on the efficiency by which cells are lysed and their protein constituents released. Standard technique to efficiently lyse Gram-negative bacteria requires mechanical disruption of the cell, and either enzymatic or chemical breakdown of the cell wall.

Extraction of proteins from extensively calcified osseous tissue, such as cortical bone has been particularly challenging for traditional methods of sample preparation. However, a comprehensive proteomic analysis of bone is only possible when the total protein constituency is effectively isolated. The efficiency of sample preparation is therefore a critical component of the analytical process. Historically, extraction of protein from bone required prolonged acid demineralization over several days to enable complete penetration of histochemical reagents to cellular components. Here we describe a method for the extraction of protein from ostrich tibia, which was used as a model sample to develop an extraction process that uses pressure cycling technology (PCT) and also which obviates the need for acid demineralization prior to extraction. The ability to extract proteins from bone without prior demineralization offers important advantages in efficient representative extraction of protein and significant time savings during sample preparation.

IntroductionThe mass extinction of the dinosaurs, marked by the Cretaceous-Tertiary boundary, pales in magnitude compared to other lesser known mass extinction events, such as the Permian-Triassic boundary. As over 99% of all of the species that ever lived are now extinct, our understanding of biological processes has been limited by what we have learned from the fewer than 1% of species that have survived more than five major mass extinction events. Recently, collagen peptides were reportedly recovered from mineralized skeletal elements of Tyrannosaurus rex and Brachylophosaurus canadensis [1,2], indicating that proteins could be preserved over geological time spans.

Pressure-enhanced proteolytic digestion exploits the ability of high hydrostatic pressure to promote protein denaturation and the access of proteolytic enzymes to their target sites. Pressure denaturation is fundamentally different from thermal denaturation as it occurs by virtue of hydration of hydrophobic

residues and by water saturation of protein substrate cavities normally inaccessible to solvent. Pressure denaturation is more efficient for hydrophobic proteins, while some hydrophilic soluble proteins are reported to retain relatively compact conformation, even when saturated by water molecules [1-6].